I've been pondering over some ideas regarding the Mangekyō, and it seems that the techniques can, in a way different from bloodlines or families of the Uchiha. All the members of a family or group over generations could possibly influence the fructification/development of all the 'known' Mangekyō techniques seen thus far. The reason for that is that the Uchiha clan conquered, and absorbed other clans during their rise to power up 'til nearly a century ago. Thus, it's perfectly sensible to conclude that their bloodline as a whole had been diluted even more than it already was due to this integration, and growth; resulting in the frequency of the Sharingan's awakening amongst them to be reduced.
However, because of the dilation and attenuation of the clan, the bloodline through many years had become diluted, which resulted in the more prestige families or "pure" families taking over for the clan. In additional to this, these families ostracized (used loosely) some of their members—in terms of breeding, away from more "diluted" members of the clan and begin breeding/reproducing with "pure" ones, causing some ocular powers to appear more frequently within these “pure” or “noble” family lines, and these are likely they represent the pinnacle of the Uchiha power—this, of course, could have resulted in rare talents like Sasuke, Itachi, Obito, and Shisui.
Basically; the theory here is like the Hyuga, the Uchiha had a main family or families—that took on the roles of leadership, and whose abilities were the pinnacle of the Uchiha power that represented the clan. These abilities are most noticeably in the Mangekyō technique, where Tsukuyomi and Amaterasu are known quite prominently, representing these pure families, and as mentioned before, these families instill in their branch sets of unequal ocular powers that are near impossible attainable by the clans that the Uchiha brought under their rule, even if bred with a “pure” Uchiha member—which represent the true height of the Uchiha. These pure families aside from inheriting an absurd amount of powerful chakra and spiritual abilities also give their children dictate the powers or affinities of that particular person —which combine with training, gives said person a Mangekyō Sharingan technique according the its possessor’s strength; allowing them to special in a power of it.
The leaders or pure families of the Uchiha enabled their offspring access to certain techniques of the Mangekyō predetermined. Tsukuyomi and Amaterasu represent the authority of power of the Uchiha; consequently meaning that while Obito and Shisui are members of a pure family, Sasuke, Itachi, and Madara come from the strongest or “purest” family of the Uchiha. Thus they retain the pinnacle of Uchiha power: Tsukuyomi and Amaterasu, and the ability to enchance its strengths.
Itachi Uchiha’s prime affinity to Genjutsu allows him to master or the Mangekyō Sharingan’s Genjutsu’s techniques such as Tsukuyomi at a level quicker than Sasuke’s.
Sasuke Uchiha’s prime affinity to Ninjutsu allows him to master the Mangekyō Sharingan’s Ninjutsu’s techniques such as Amaterasu; at a level quicker higher than Itachi’s.
Madara Uchiha, unlike the first two, has no preset affinity (besides Katon). However, by exercising Susano’o, his Mangekyō Sharingan’s (not Eternal)  presumably is balanced in terms of Ninjutsu properties and Genjutsu properties; having Mugen Tsukuyomi as the technique for governing the world.